Application of fuzzy logic principles to the classification of 2D-PAGE maps belonging to human pancreatic cancers treated with Trichostatin-A

Marengo, Emílio; Robotti, Elisa; Cecconi, Daniela; Scarpa, Aldo; Righetti, Pier Giorgio

doi:10.1109/fuzzy.2004.1375749

Cited by 6 publications

(7 citation statements)

References 26 publications

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“…Results of proteomic differential analysis have been published (4); here we followed a complementary approach aimed at discriminating the categories involved and avoiding the step of matching through the application of a strategy that considers the overall impression of the gel. In recent years a similar classification approach that considers the overall pattern that emerges from gel images without spot detection has been explored for many different data sets (5)(6)(7)(8). This method tries to capture the essential information of a gel image through the use of a set of descriptors obtained from the assessment of the pixel values in different quadrants of the image obtained by a regular grid.…”

Section: Introductionmentioning

confidence: 99%

An Integrated Strategy in Two-Dimensional Electrophoresis Analysis Able to Identify Discriminants Between Different Clinical Conditions

Pattini

Mazzara

Conti

et al. 2008

Exp Biol Med (Maywood)

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Two-dimensional gel electrophoresis (2DE) is an indispensable tool in proteomics for the analysis of protein expression in complex biological systems such as cells and tissues. However, the automatic extraction of information from gel images is still a challenging task. In this paper we propose a strategy that represents a computational procedure of support to the discrimination of different clinical conditions associated with the samples. The analyzed gel images were acquired within the framework of a study of peripheral neuropathies: twenty-four 2DE maps generated from cerebrospinal fluid (16 pathologic and 8 control subjects) were processed. Quantitative features were defined to describe each image and treated with a method of dimensionality reduction. The informativeness of the descriptors allowed us to see the gel of the data set as items in a three-dimensional space, segregating according to the clinical conditions. Moreover, information with prognostic value was obtained for a single outsider gel of a patient who was included in a clinical subgroup at the first diagnosis but whose disease progressed with clinical features belonging to a different clinical subgroup. The method developed may represent an effective tool of classification that can be used repeatedly to capture the essential impression from separation images.

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Section: Introductionmentioning

confidence: 99%

An Integrated Strategy in Two-Dimensional Electrophoresis Analysis Able to Identify Discriminants Between Different Clinical Conditions

Pattini

Mazzara

Conti

et al. 2008

Exp Biol Med (Maywood)

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“…Although not yet elaborated into commercially available software packages, these methods appear to be just as powerful and user friendly. In one approach, as reported by Marengo et al [26][27][28][29], statistical treatment of 2-D maps is performed via fuzzy logics [30].…”

Section: Home-made Approaches: Fuzzy Logicsmentioning

confidence: 99%

Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

et al. 2005

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The present review attempts to cover a number of methods that have appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this review to conventional two-dimensional (2-D) map analysis which couples orthogonally a charge-based step (isoelectric focusing) to a size-based separation step (sodium dodecyl sulfateelectrophoresis). The first and oldest method applied to 2-D map data reduction is based on statistical analysis performed on sets of gels via powerful software packages, such as Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately running a number of replicas for control and treated samples. The two sets of data are then merged and compared via a number of software packages which we describe. In addition to commerciallyavailable systems, a number of home made approaches for 2-D map comparison have been recently described and are also reviewed. They are based on fuzzyfication of the digitized 2-D gel image coupled to linear discriminant analysis, three-way principal component analysis or a combination of principal component analysis and soft-independent modeling of class analogy. These statistical tools appear to perform well in differential proteomic studies.

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“…Finally, it should be noted that, whereas, up to the present, in most studies of expression proteomics, univariate statistical tests, such as the Student's t-test (PD-Quest software), have been used for identifying protein expression by looking for significant changes from one group to another for each protein spot, a multivariate approach, which considers data globally, as here described and first proposed by Marengo et al [41][42][43][44] in 2003, appears today to be a more robust alternative. A recent study by Karp et al [53] has in fact shown, in agreement with our data, that multivariate statistical tools have the advantage of reducing the risk of false positives and of identifying spots that are significantly altered in terms of correlated expression rather than absolute expression values.…”

Section: Discussionmentioning

confidence: 98%

“…Our research group has recently developed new methods for the comparison of classes of 2-D PAGE maps based on fuzzy logic [41][42][43][44]; PCA coupled to cluster analysis and classification procedures have been applied [45,46] as well. Here, an application of PCA coupled to classification methods, to a dataset consisting of ten samples belonging to two human lymphoma cell lines, is presented.…”

Section: General Aspectsmentioning

confidence: 99%

Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two‐dimensional gel electrophoresis

et al. 2006

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Mantle cell lymphoma (MCL) cell lines have been difficult to generate, since only few have been described so far and even fewer have been thoroughly characterized. Among them, there is only one cell line, called GRANTA-519, which is well established and universally adopted for most lymphoma studies. We succeeded in establishing a new MCL cell line, called MAVER-1, from a leukemic MCL, and performed a thorough phenotypical, cytogenetical and molecular characterization of the cell line. In the present report, the phenotypic expression of GRANTA-519 and MAVER-1 cell lines has been compared and evaluated by a proteomic approach, exploiting 2-D map analysis. By univariate statistical analysis (Student's t-test, as commonly used in most commercial software packages), most of the protein spots were found to be identical between the two cell lines. Thirty spots were found to be unique for the GRANTA-519, whereas another 11 polypeptides appeared to be expressed only by the MAVER-1 cell line. A number of these spots could be identified by MS. These data were confirmed and expanded by multivariate statistical tools (principal component analysis and soft-independent model of class analogy) that allowed identification of a larger number of differently expressed spots. Multivariate statistical tools have the advantage of reducing the risk of false positives and of identifying spots that are significantly altered in terms of correlated expression rather than absolute expression values. It is thus suggested that, in future work in differential proteomic profiling, both univariate and multivariate statistical tools should be adopted.

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Application of fuzzy logic principles to the classification of 2D-PAGE maps belonging to human pancreatic cancers treated with Trichostatin-A

Cited by 6 publications

References 26 publications

An Integrated Strategy in Two-Dimensional Electrophoresis Analysis Able to Identify Discriminants Between Different Clinical Conditions

An Integrated Strategy in Two-Dimensional Electrophoresis Analysis Able to Identify Discriminants Between Different Clinical Conditions

Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two‐dimensional gel electrophoresis

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